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| Status |
Public on Jan 25, 2018 |
| Title |
WT-biological replicate 2-technical replicate 2 |
| Sample type |
SRA |
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| Source name |
bone marrow derived mast cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: bone marrow derived mast cell
strain: C57BL/6
genotype: wild type
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| Growth protocol |
Mouse bone marrow cells were isolated from femurs and cultured in RPMI1640 medium plus 10% (vol/vol) FBS (Gibco) with 10 ng/ml IL-3 and 5 ng/ml SCF. Half of the medium was replaced by fresh medium with cytokines every 2–3 d during culture. After 4–6 wk in culture, BMMCs were stained to confirm the surface expression of FcɛRI and c-Kit. Cells with purity >97.5% were used for subsequent experiments.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were isolated by Trizol reagent. Poly-A tailed RNAs were enriched by GenElute™ mRNA Miniprep Kit (MRN70-1KT, Sigma). The mRNAs were treated with TURBO DNase, purified by a RNeasy MinElute Cleanup Kit (QIAGEN). Treated mRNAs with 0.5% unmethylated RNA controls from lambda genome were bisulfite converted using the EZ RNA Methylation kit (R5001, Zymo Research). Briefly, 500 ng mRNA was converted using three cycles of 10-min denaturation at 70℃ followed by 45min at 54℃. RNA separation from bisulfite solution, desulfonation, and purification were performed following the standard protocol of the kit.
Strand-specific libraries were constructed following the “TruSeq stranded mRNA sample preparation guide” from illumina for 150PE sequencing using Hiseq3000.
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| Library strategy |
Bisulfite-Seq |
| Library source |
transcriptomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Description |
FcɛRI+ c-Kit+, purity >97.5%
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| Data processing |
Illumina Casava1.6 software used for basecalling.
Reads mapping and methylcytosine calling were analyzed by BS-RNA using converted mm10 and lambda genome as references.
BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data. Computational biology and chemistry, doi:10.1016/j.compbiolchem.2016.09.003 (2016).
Splice sites information was added using refGene.gtf file during read mapping.
Cs with methylation rate above 0.1 and at least two reads supporting methylation in both technical and biological replicates of one group and below the non-conversion rate of each of the replicates of the other group (WT1-rep1:0.0015, WT1-rep2:0.0015, KO1-rep1:0.0017, KO1-rep2:0.0016, WT2-rep1:0.0012, WT2-rep2:0.0013, KO2-rep1:0.0012, KO2-rep2:0.0012,) were chosen as group-specific Cs.
Genome_build: GRCm38/mm10
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| Submission date |
Jul 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qian Zhang |
| E-mail(s) |
oilpangpang@hotmail.com
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| Phone |
+8615921196443
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| Organization name |
Second military medical university
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| Street address |
xiangyin road 800
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| City |
shang hai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE100719 |
Distinct 5-methylcytosine profiles in poly(A)RNA from mouse bone marrow derived mast cells |
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| Relations |
| BioSample |
SAMN07311767 |
| SRA |
SRX2978630 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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